October 14, 2011

Biological activities database schema

In my day job I'm currently redesigning our database for biological activities of chemicals in preparation for our next big project that will hopefully start with a HTS within this year.
From the experiences I/we have had of our last system, I would like this one to be able to capture the raw data better, and then we would have software to calculate and visualize the end points (like percentage of control, fold change, EC50, etc.).
My idea is to base this on plates (with a generous definition of a plate that could also hold for example a set of cages with animals...) and experiments. I have attached an example DB schema to this post, click the image to enlarge to a zoomable version, or click here to download it as an MySQL Workbench document. Each well in the plate is marked as being positive or negative control, empty, or holding a test compound. There should also be information about everything that is put into it, such as cells, cofactors, stimulants, blockers, etc, and finally, there should be readouts, with the possibility to record time series.

If you have any comments, like the setup, or have ideas as to how this approach could be improved, please let me know in the comments.

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